|
|
@ -77,7 +77,7 @@ ui <- fluidPage( |
|
|
|
htmlOutput("report"), |
|
|
|
h3("Nitrogen"), |
|
|
|
tableOutput("nitrogen"), |
|
|
|
plotOutput("visorplot") |
|
|
|
plotOutput("visorplot", height = "1000px") |
|
|
|
) |
|
|
|
), |
|
|
|
|
|
|
@ -831,7 +831,7 @@ server <- function(input, output) { |
|
|
|
if (input$nhc == 3){ |
|
|
|
pops<-sqlFetch(dta, "POPULATIONS") |
|
|
|
|
|
|
|
pops %>% dplyr::filter(samples == input$id) %>% gather(pop,value,-samples) %>% |
|
|
|
g_pop<-pops %>% dplyr::filter(samples == input$id) %>% gather(pop,value,-samples) %>% |
|
|
|
mutate(pop=factor(pop, levels=c("CD45pos_Alive","T_cells","CD8","CD4","DN","NK", "B_cells", |
|
|
|
"CD45neg_LDneg","EpCAMneg_HLAIneg","EpCAMneg_HLAIpos","EpCAMpos_HLAIpos"))) %>% |
|
|
|
ggplot(aes(pop, value))+ |
|
|
@ -839,6 +839,36 @@ server <- function(input, output) { |
|
|
|
labs(title = input$id, y="% parent", x="")+ |
|
|
|
theme_bw()+ |
|
|
|
theme(axis.text.x = element_text(angle=90, hjust=1, vjust=0.5)) |
|
|
|
tl<-sqlFetch(dta, "IC") %>% filter(samples == input$id) |
|
|
|
|
|
|
|
mtl<-melt(tl, variable.name = "Receptors") |
|
|
|
mtl$Receptors<-as.character(mtl$Receptors) #Para poder depurar bien el texto, lo pasamos a tipo character |
|
|
|
mtl$Receptors<-gsub("n","-",mtl$Receptors, fixed = T) |
|
|
|
mtl$Receptors<-gsub("p","+",mtl$Receptors, fixed = T) |
|
|
|
mtl$Receptors<-gsub("_"," ",mtl$Receptors) |
|
|
|
mtl[mtl$value < 1, "Receptors"]<-"Other" |
|
|
|
mtl$Receptors<-gsub("[A-Z]*-*[0-9T]- *", "", mtl$Receptors) |
|
|
|
mtl$Receptors<-gsub("+ $", "", mtl$Receptors) |
|
|
|
mtl$Receptors[mtl$Receptors == ""]<-"All Negative" |
|
|
|
|
|
|
|
mtl$Receptors<-factor(mtl$Receptors) |
|
|
|
mtl$Population<-factor(mtl$Population, levels = c("CD8", "CD4")) |
|
|
|
|
|
|
|
# colorCount<-length(unique(mtl$Receptors)) |
|
|
|
# getPalette = colorRampPalette(RColorBrewer::brewer.pal(12, "Set3")) |
|
|
|
|
|
|
|
color<-c(c("CTLA4+ LAG3+ PD1+ TIGIT+ TIM3+"="black","All Negative"="white","Other"="grey50", "PD1+"="#C07AFF", "CTLA4+"="#3EB3DE","TIM3+"="#5EF551","LAG3+"="#DEBB3E","TIGIT+"="#FA7055"), |
|
|
|
c("CTLA4+ PD1+"="#6666FF","PD1+ TIM3+"="#849CA8", "LAG3+ PD1+"="#C47F9F","PD1+ TIGIT+"="#D259AA", "CTLA4+ TIM3+"="#4ED498", "CTLA4+ LAG3+"="#8EB78E", "CTLA4+ TIGIT+"="#9C929A", "LAG3+ TIM3+"="#9ED848", "TIGIT+ TIM3+"="#ACB353", "LAG3+ TIGIT+"="#EC964A"), |
|
|
|
c("CTLA4+ PD1+ TIGIT+"="#B86B6A","CTLA4+ PD1+ TIGIT+ TIM3+"="#B81515","LAG3+ PD1+ TIGIT+"="#007D8A", "PD1+ TIGIT+ TIM3+"="#D64545", "LAG3+ PD1+ TIGIT+ TIM3+"="#0f5860", "LAG3+ TIGIT+ TIM3+"="#50cad3")) |
|
|
|
|
|
|
|
g_IC<-ggplot(mtl, aes(samples, value, fill=Receptors))+ |
|
|
|
geom_bar(stat="summary", fun="sum",color="black")+ |
|
|
|
labs(x="Patient", y="% CD8+", fill="")+ |
|
|
|
facet_grid(.~Population)+ |
|
|
|
scale_fill_manual(values = color[levels(mtl$Receptors)[levels(mtl$Receptors) %in% unique(mtl$Receptors)]])+ |
|
|
|
theme_bw()+ |
|
|
|
theme(axis.text.x=element_text(angle=45, hjust=1)) |
|
|
|
ggpubr::ggarrange(g_pop, g_IC, heights = c(0.4, 0.6), ncol = 1) |
|
|
|
} |
|
|
|
}) |
|
|
|
|
|
|
|